org.proteios.io.mzdata
Class MzDataExpProcessingMethodBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataExpCommon
      org.proteios.io.mzdata.MzDataExpCommonDc
          org.proteios.io.mzdata.MzDataExpCommonAnnotation
              org.proteios.io.mzdata.MzDataExpCommonPeakListSet
                  org.proteios.io.mzdata.MzDataExpProcessingMethodBlock

public class MzDataExpProcessingMethodBlock
extends MzDataExpCommonPeakListSet

This class supports export of mzData files from Proteios. An mzData file contains information on a mass spectrometry experiment. Given a Proteios peakListSet, MzDataExporter fetches stored data related to this peakListSet and stores it in an mzData file.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-09-19 11:38:54 +0200 (Tue, 19 Sep 2006) $

Field Summary

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

anna, dc, factory

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommon

log

Constructor Summary

MzDataExpProcessingMethodBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchDataProcessingStepAnnotations(DataProcessingStep dataProcessingStep) Fetches variable values stored as annotations for dataProcessingStep.
void	write(XMLCrudeWriter xmlCrudeWriter, DataProcessingStep dataProcessingStep) Creates a processingMethod block.

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonPeakListSet

getPeakListSet, setPeakListSet

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonAnnotation

createAddedParamAnnotationType, createAnnotationType, createCvLookupAnnotationType, createCvParamAnnotationType, createUserParamAnnotationType, fetchAddedParamAnnotationType, fetchAnnotation, fetchCvLookupAnnotation, fetchCvLookupAnnotationList, fetchCvLookupAnnotationType, fetchCvParamAnnotation, fetchCvParamAnnotationList, fetchUserParamAnnotation, fetchUserParamAnnotationList, obtainAddedParamAnnotationType, obtainCvLookupAnnotationType, storeAnnotation, storeCvLookupAnnotation, storeCvParamAnnotation, storeUserParamAnnotation

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

enableAnnotator, enableDbControl, enableDbControl, getDbControl, getSessionControl, setDbControl

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommon

getBlockTagName, setBlockTagName, write, writeAttribute, writeEndTag, writeNamespace, writeSimpleElementPair, writeSimpleElementPair, writeSingleElementEnd, writeStartElement, writeStartElementEnd, writeStartListTag, writeStartTag, zeroPad, zeroPad, zeroPad

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MzDataExpProcessingMethodBlock

public MzDataExpProcessingMethodBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

write

public void write(XMLCrudeWriter xmlCrudeWriter,
                  DataProcessingStep dataProcessingStep)
           throws javax.xml.stream.XMLStreamException

Creates a processingMethod block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

dataProcessingStep - DataProcessingStep dataProcessingStep used

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

fetchDataProcessingStepAnnotations

public void fetchDataProcessingStepAnnotations(DataProcessingStep dataProcessingStep)

Fetches variable values stored as annotations for dataProcessingStep.

Parameters:

dataProcessingStep - DataProcessingStep dataProcessingStep used